CA2321438A1

CA2321438A1 - Treating cancer

Info

Publication number: CA2321438A1
Application number: CA002321438A
Authority: CA
Inventors: Hilmar Meek Warenius; Laurence Anthony Seabra
Original assignee: Individual
Current assignee: Theryte Ltd
Priority date: 1998-02-18
Filing date: 1999-02-18
Publication date: 1999-08-26
Also published as: EP1057030A2; DE69907154T2; AU2630099A; WO1999042834A3; EP1057030B1; CA2321482A1; AU2537999A; WO1999042821A3; AU2538599A; ATE238556T1; AU2538099A; CA2321481A1; AU743454B2; EP1057033A1; DE69907156T2; WO1999042090A2; EP1057032B1; AU2538199A; WO1999042090A3; ATE238557T1

Abstract

Provided is a method for selecting a chemotherapeutic agent for treating cancer, which method comprises: (a) testing a sample comprising cells that substantially do not express p21 and/or in which p21 protein is substantially undetectable, or an extract therefrom for the level of expression of Cyclin D1 of for the abundance of Cyclin D1 protein; and (b) if Cyclin D1 is over expressed, and/or Cyclin D1 protein is present at elevated levels, selecting for treatment a chemotherapeutic agent comprising a taxane; (c) if Cyclin D1 is not over expressed and/or Cyclin D1 protein is substantially not present at elevated levels, selecting for treatment a chemotherapeutic agent comprising an agent other than a taxane. Also provided is a kit for selecting a chemotherapeutic agent for treatment, which kit comprises: (a) a means for identifying cells in which p21 is substantially not expressed and/or p21 protein is substantially undetectable; and (b) a means for testing for the level of expression of Cyclin D1 or for the abundance of Cyclin D1 protein in cells or in a sample therefrom.

Description

TREATING CANCER
The present invention concerns a method for selecting the most appropriate therapy for patients suffering from cancer. The invention is particularly concerned with selecting a chemotherapeutic agent for treating cancer. The invention is particularly useful for choosing between a treatment agent comprising a platinating agent and a treatment agent comprising a taxane such as Paclitaxel (taxol).
Although radiotherapy and chemotherapy have been responsible for curing many people of cancer in the latter half of this century, there still remain a large number of tumours which either show little response to treatment, or respond initially only to recur later. In particular, women treated for ovarian cancer with platinating agents often show encouraging initial responses to chemotherapy (which in the UK usually involves the use of cis-diamminedichloroplatinum (CDDP) as the drug of first choice), but by 5 years after diagnosis, 2/3 of them have succumbed to their disease. Similarly Lung cancer patients may respond favourably to combination chemotherapy regimens containing CDDP at the outset of treatment but very few experience long term survival. A better understanding of the mechanisms underlying the responsiveness of cancers to CDDP, could help predict which patients are most likely to benefit from CDDP or whether alternative cytotoxic agents such as taxanes (e.g. taxol) or different therapies such as radiotherapy might be appropriate. Understanding treatment response mechanisms also holds the possibility of selectively modulating these mechanisms to improve the treatment of human cancer using CDDP.
It has become increasingly apparent that certain oncogenes and tumour suppressor genes, and genes responsible for the molecular control of proliferating cells proceeding through the cell division cycle (cell cycle), may not only be implicated in carcinogenesis, but can also influence the sensitivity of malignant cells to therapeutic agents.
Attempts have therefore been made to use these and other genes to try and predict the therapeutic response of human cancer to the presently available treatment modalities such as radiotherapy andlor cytotoxic chemotherapy. Research up to the present time, however, has generally attempted to only examine the expression of single tumour related genes as SU8ST1TUTE SHEET (RULE 26) methods of predicting therapeutic response. Research in the public domain has suggested that mutations in the p53 tumour suppressor gene, which can be found in around 50% of common cancers such as those of the breast, lung and ovary, are associated with resistance to treatment with cytotoxic drugs or radiation. Despite a considerable body of work, however, there are at present no successful clinical tests by which the detection of mutations in the p53 gene alone can be used to predict with an acceptable degree of certainty whether or not a patient's cancer is likely to respond to chemotherapy with, for example, platinating agents or the newer cytotoxic agents such as taxanes.
The effect of the expression of single genes alone on the response of human cancer cell lines to treatment with cytotoxic drugs such as CDDP has been studied in human in vitro cell lines because these present a model system relevant to the response of human cancer in the clinic. In particular, they exhibit the range of sensitivities to cytotoxic drugs and ionising radiation usually encountered in the clinic. Discoveries in human in vitro cell lines, therefore, have a strong possibility of being able to be translated into clinically useful tests far how well cancers may be expected to respond to treatment.
The progress of cells through the cell cycle is governed by holoenzymes formed by a combination of proteins called cyclins, whose levels fluctuate throughout the cell cycle, and cyclin dependent kinases (CDKs) which become active when they join with cyclins.
The cyclin/CDK complexes can be inhibited by proteins termed cyclin dependent kinase inhibitors (CDKIs) which include the protein p21 WAF 1/CIP 1 (p21 ).
The protein products of the cyclin D 1 and B 1 genes and their respective cyclin-dependent kinase partners CDK4 and CDK1 have been studied. Cyclin D1 and CDK4 control the progress of cells through the cell cycle checkpoint between G1 and S-phase {the phase of DNA synthesis). Cyclin B1 and CDK1 control the cell cycle checkpoint just before mitosis. The expression of cyclin D1 protein in a series of 16 human cancer cell Iines has been shown to be related to their intrinsic resistance to the cytotoxic drug CDDP
(Warenius et al., 1996). Cyclin D1 protein levels, however, showed no relationship with radiosensitivity, another treatment modality. The relationship between cyclin D 1 and SUBSTITUTE SHEET (RULE 26) CDDP resistance is not, however, strong enough on its own to provide the basis of clinically useful predictive assays.
Paclitaxel, which is a member of the class of anti-cancer drugs known as taxanes, has been shown clinically to be of benefit when added to treatment with platinating agents in the clinical treatment of ovarian cancer. It has been reported that cells can become more sensitive to Paclitaxel when they lose normal p53 function as a result of infection with human papilloma virus constructs or SV40 virus constructs (Wahl et al, Nature Medicine, vol. 2, No. 1, 72-79, 1996). This is thought to result from increasing G2/M
arrest and apoptosis. However, it is not the case that all p53 mutant cancer cells are sensitive to taxol. Accordingly, based on this correlation on its own these studies have not been able to engender a reliable predictive method for determining a likely effective treatment in specific cases.
It is an aim of the present invention to solve the problems associated with the prior art and to provide a method which can be used to predict a specific treatment which is likely to be successful in specific cases.
Thus, this invention provides methods of predicting whether human cancer cells are best treated with taxanes such as taxol or with other agents such as CDDP, by contemporaneously measuring the properties of two or more cancer-related genes.
Moreover, the co-relationship between certain independently expressed cancer genes identified in this invention also provides previously undescribed targets to which a therapy that is more cancer specific can potentially be directed.
SUBSTITUTE SHEET (RULE 26) In particular, this invention provides a method for selecting a chemotherapeutic agent for treating cancer, which method comprises:
(a) testing a sample comprising cells that substantially do not express p21 and/or in which p21 protein is substantially undetectable, or an extract therefrom for the level of expression of Cyclin D1 or for the abundance of cyclin Dl protein; and (b) if cyclin D1 is overexpressed, andlor cyclin D1 protein is present at elevated levels, selecting for treatment a chemotherapeutic agent comprising a taxane;
(c} if cyclin D1 is not overexpressed andlor cyclin D1 protein is substantially not present at elevated levels, selecting for treatment a chemotherapeutic agent comprising an agent other than a taxane.
The over-expression of Cyclin D1, or the elevation of Cyciin D1 protein levels can be measured by any appropriate method, e.g. Western blotting. The point at which it is considered that the level is elevated or that the expression is over-expression is clear to the skilled person in this field, according to general teaching from the literature regarding usual levels of cyclin D1 in human cell lines (see Oncogene, 1993, vol. 8, 2127-2122; and Oncogene, 1995, vol. 10, 775-778). This point can be determined according to the judgement of the individual carrying out the present method, depending on the particular cancer cells and patient involved.
Similarly, the expression of p21, or the level of p21 protein can be measured by any appropriate method, including methods corresponding to those referred to above for measuring Cyclin D1 levels. Specifically, p21 is a cyclin dependent kinase inhibitor which can be detected by Western blotting, immunocytochemistry or newer developing techniques, such as determining the relative abundance of p21 mRNA. The point at which it is considered that the p21 is effectively not expressed (or the expression is not elevated) or the p21 protein is effectively not detectable {or is effectively not elevated) is clear to the skilled person in this field, according to general teaching from the literature regarding usual levels of p21 in human cell lines (see Oncogene, 1995, vol. 11, 2021-2028; and Oncogene, 1996, vo1.12(6), 1319-1324).
SUBSTITUTE SHEET (RULE 26) This application also provides a kit for selecting a chemotherapeutic agent for treatment, which kit comprises:
(a) a means for identifying cells in which p21 is substantially not expressed and/or p21 protein is substantially undetectable; and (b) a means for testing for the level of expression of Cyclin D 1 or for the abundance of cyclin D 1 protein in cells or in a sample therefrom.
The present invention is advantageous, since previously there were no indicators that simultaneously measuring the mutational status and/or levels of expression of the protein products of two or more oncogenes, proto-oncogenes or tumour suppressor genes in human cancer cells would be able to provide the basis of a reliable clinical test for whether clinical tumours were best treated with taxanes, or with alternative agents.
Thus using the present invention, in appropriate cases chemotherapeutic agents other than taxanes, such as CDDP, can be ruled out of the treatment regime before treatment begins and replaced with taxanes, such as taxol. This has the advantage of avoiding unnecessary treatment which might be harmful to the patient and also saves money by finding the correct treatment more quickly. In addition, the patient receives the right treatment earlier in the procedure, saving time which is vital for the patient's chances of recovery.
The present invention specifically deals with measuring the levels of Cyclin D
1 protein, in cells in which p21 WAF 11CIP 1 protein levels have been assayed. High cyclin D 1 levels or high cyclin D1 expression together with substantially undetectable p21 protein levels is indicative of a resistance to the cytotoxic effects of a chemotherapeutic agent other than a taxane (e.g. platinating agents such as CDDP) and is also strongly associated with a sensitivity to taxanes. Thus, as cyclin D 1 levels rise, whilst the cells are more likely to be resistant to platinating agents, they remain highly likely to be sensitive to taxanes (see Figure 1 ).
The present invention will be described in further detail by way of example only with reference to the accompanying drawings, in which:
SUBSTITUTE SHEET (RULE 26) WO 99142835 PC'T/GB99/00501 Figure 1 shows the relationship between the resistance to Cisplatin (black points) and the resistance to taxanes (white points) in cell lines in which p21 WAF1/CIP1 protein levels were substantially undetectable; and Figure 2 shows the corresponding relationship in cell lines in which p21 protein levels were detectable.
Human cancer cell Iines with a combination of substantially undetectable p21 protein levels and high levels of expression of the cyclin D 1 protein are resistant to the cytotoxic effects of chemotherapeutic agents such as CDDP, but are sensitive to taxanes.
These findings carry important clinical possibilities with regard to providing a potentially new parameter for predictive assays for taxane responsiveness or a new target for modulating taxane responsiveness.
The high correlation of taxane sensitivity to CDDP resistance in cells with substantially absent p21 protein, and high cyclin D1 levels or cyclin D1 over-expression also provides a potential target for drug development. Efforts are being made to develop drugs against cyclin D 1. Such drugs are likely to be more effective when used together to treat cancers with the above p21 levels and cyclin DI over-expression. Such drugs might also be used in combination with other agents such as taxol as potentiators of its effectiveness.
Figure 1 shows that in cell lines with undetectable p21 and high cyclin D1 levels or cyclin D 1 over-expression there is a strong relationship between resistance to CDDP
and sensitivity to taxol, as measured by the D0.1 values (the dose of the drug which reduces clonogenic survival to 10% of the control, untreated cells). Thus human cancer cells with undetectable p21 and high levels of cyclin D1 protein which do not respond to CDDP will very likely respond to taxanes as an alternative therapy. The cyclin D l Ip21 mutation test may also indicate a correlation of taxane sensitivity to resistance to other cytotoxic drugs such as etoposide.
SUBSTITUTE SHEET (RUE.E 26) A clinical test may be developed for taxane sensitivity based on the measurement of Cyclin D I protein expression and the presence of p21. Cyclin D 1 protein is typically measured by Western blotting or immunocytochemistry.
A specific example of a chemotherapeutic agent, the resistance against which is often compared with taxane sensitivity, is CDDP. Thus using the present invention, in appropriate cases CDDP can be ruled out of the treatment regime before treatment begins and replaced with taxol. Further examples of agents which can be replaced with taxanes include other platinating agents, such as carboplatin and paraplatin as well as other chemotherapeutic agents, for example alkylating agents, DNA intercalating agents such as Doxorubicin, topoisomerase inhibitors, anti-metabolites such as methotrexate, 5-fluorouracil, DNA synthesis inhibitors such as cytosine arabinoside, and mitotic inhibitors such as the vinca alkaloids.
Because cyclin D 1 is a relatively short lived protein under cyclical transcriptional control, it is likely that mRNA levels for cyclin D1 follow the same pattern as the cyclin D1 protein and show a similar strong relationship to CDDP resistance. This makes it possible to carry out a functional assay for resistance to CDDP by extracting mRNA from tumour samples and using this to determine the relative abundance of cyclin D
1 mRNA
and to detect mutations in the p53 mRNA.
As regards p2I/WAF1/CIP1, this is a cyclin dependent kinase inhibitor which can be detected by Western blotting, immunocytochemistry or newer developing techniques, such as determining the relative abundance of p21 mRNA.
Oligonaccleotide Arrays Determination of mRNA levels can be effected in a number of ways. One can readily convert poly-A bearing mRNA to cDNA using reverse transcription - a method is described in the example illustrating this invention. Reverse Transcriptase PCR
(RTPCR) methods allow the quantity of single RNAs to be determined, but with a relatively low level of accuracy. Arrays of oligonucleotides are a relatively novel approach to nucleic acid analysis, allowing mutation analysis, sequencing by SUBSTITUTE SHEET (RULE 26) hybridisation and mRNA expression analysis. Methods of construction of such arrays have been developed, ( see for example: A.C. Pease et al. Proc. Natl. Acad.
Sci. USA. 91, 5022 - 5026, 1994; U. Maskos and E.M. Southern, Nucleic Acids Research 21, 2270, 1993; E.M. Southern et al, Nucleic Acids Research 22, 1368 - 1373, 1994) and further methods are envisaged. Arrays that measure expression levels of mRNAs and detect mutations in those RNAs are being developed and these offer an attractive embodiment of the diagnostic test proposed by this invention.
Immunocytochemistry An alternative embodiment of this invention can measure Cyclin D 1 protein levels by immunocytochemistry using confocal laser fluorescence microscopy. Preferably a scanning system is used such as those described in PCT/US91/09217, PCTINL/00081 and PCT/US95/O1886. Additionally, it is desirable that the microscopy system is also able to analyse multiple fluorescent dyes. Antibodies against p21 are labelled with one dye, an antibody against cyclin DI (sc-6281, Santa Cruz Biotechnology, CA) is labelled with a second dye whilst a third DNA binding dye can be used to select for aneuploid cells.
DNA binding dyes such as Hoechst 33258 dye, which binds AT-rich DNA or Chromomycin A3, which binds GC-rich DNA, are appropriate.- A diagnostic test may comprise the steps of:
~ Extracting a biopsy of the tumour from a patient.
~ Optionally micro-dissecting that material to separate normal tissue from tumour material.
~ Preparing the biopsy material for microscopy which includes the steps of:
Labelling the biopsy material with the above fluorescently labelled antibody probes against Cyclin D 1. The biopsy material may also, optionally be labelled with antibody probes against p21 protein and with a DNA binding dye.
~ Separating the labelled cells from unbound labelled probes.
Placing the labelled biopsy material in a scanning confocal microscope to count cells that:
~ Over-express or show elevated levels of cyclin D1, i.e. are labelled with at least a threshold quantity of antibody against cyclin D 1.
SUBSTITUTE SHEET (RULE 26) Optionally, do not express p21, i.e. are labelled with below a threshold quantity of antibodies against p21. Alternatively, p21 levels might be determined by analysis of the mRNA as discussed above.
~ Optionally, have chromosomal amplifications as detected by the intensity of fluorescence from DNA binding fluorescent dyes.
Fluorescence Activated Cell Sorting A further embodiment of the diagnostic test can exploit Fluorescence Activated Cell Sorting (FACS). A FACS instrument separates cells in a suspension in a manner dependent on the cells being labelled with a fluorescent marker. A typical FACS device operates as follows. Cells in a suspension travelling in single file are passed through a vibrating nozzle which causes the formation of droplets containing a single cell or none at all. The droplets pass through a laser beam. Fluorescence excited from each individual cell in its droplet by the laser is measured. After the detector the stream of cells in suspension pass through an electrostatic collar which gives the droplets a surface charge.
The cells carrying droplets are given a positive or negative charge. If the drop contains a cell that fluoresces with an intensity above a particular threshold, the drop gets a charge of one polarity. Unlabelled cells get a charge of the opposite polarity. The charged droplets are then deflected by an electric field and depending on their surface charge are directed into separate containers and are counted Droplets that contain more than one cell scatter light more than individual cells which is readily detected and so these are left uncharged and enter a third disposal container. Multi-channel fluorescent detection devices have been constructed that can separate cells on the basis of labelling with multiple different fluorescent labels. These have multiple lasers which can excite fluorescence at different frequencies and the detector will detect different emission frequencies. A three label system is appropriate for this test. The same labelled probes as those described above for use in a confocal scanning fluorescence microscope would be appropriate. A diagnostic test might comprise the steps of:
~ Extracting a biopsy of the tumour from a patient.
~ Optionally micro-dissecting that material to separate normal tissue from tumour material.
~ Disrupting intracellular adhesion to form a single cell suspension.
SUBSTITUTE SHEET (RULE 26) WO 99/42$35 PCT/GB99/00501 ~ Labelling the suspended cells with the above fluorescently labelled probes against cyclin D1. The biopsy material may also, optionally be labelled with antibody probes against p21 and with a DNA binding dye.
~ Separating the labelled cells from unbound labelled probes.
~ Passing the labelled cell suspension through a FACS device to count cells that:
Over-express or show elevated levels of cyclin D1, i.e. are labelled with the anti-cyclin D 1 antibody above a threshold for 'normal' expression.
~ Optionally, do not express p21, i.e. are labelled with below a threshold quantity of antibody against p21.
Optionally, have chromosomal amplifications as detected by the intensity of fluorescence from DNA binding fluorescent dyes.
Modulation of Cyclin Dl Expression in Human Cancers not expressing p21 At present many attempts are being made to develop drugs which inhibit cyclin D 1. As this molecule has a vital function in controlling the progress of normal cells through the 'start' component of the G1/S checkpoint such inhibitors would be likely to be extremely non-selective and very toxic to normal cells. The more specific relationship of resistance to CDDP and sensitivity to taxanes in cancer cells not expressing p21 and having elevated cyclin D 1 levels described here provides a much more defined target for novel therapeutic agents which could potentially used in conjunction with taxanes, this being an agent with a proven track record of curing many (though by no means all) cancers. This approach is based on a concept of starting with therapeutic agents which already work to some extent and using techniques such as gene targeting to enhance the efficacy of already available therapeutic agents.
In the case of patients who do not express p21, it may be possible to increase their responsiveness to platinating agents by decreasing their levels of cyclin D1.
Cyclin D1 inhibitors are likely to be non-selectively toxic, but if administered at low doses in conjunction with an agent such as a taxane, the combination may be more effective against tumours than either alone, particularly to cells overexpressing cyclin D 1.
SUBSTITUTE SHEET (RULE 26) Examples Human in vitro cell lines of different histological origin which exhibit a range of intrinsic sensitivities to cytotoxic drugs as measured by clonogenic cell survival assays, have been shown to provide appropriate models for the response of clinical tumours to chemotherapy. In particular, these cell lines exhibit the range of sensitivities to cytotoxic drugs and ionising radiation usually encountered in the clinic. These human in vitro cancer cell lines are now widely recognised as relevant models for the clinical response of tumours to chemotherapy. Intrinsic sensitivity to cytotoxic agents is measured by clonogenic assays of a range of human cancer cell lines. It is therefore possible to identify genes whose expression and/or mutational status is related to intrinsic sensitivity to cytotoxic agents in a wide range of human in vitro cell lines by measuring the expression of target genes and/or determining their mutational status and correlating these parameters to cell line sensitivity to cytotoxic agents. This procedure has identified genes relevant to clinical responsiveness to CDDP. Discoveries in human in vitro cell lines, such as those leading to this invention, therefore, can be translated into clinically useful tests for how well cancers may be expected to respond to treatment. The experimentation that has been undertaken to measure the clonogenic cell survival of a wide range of human in vitro cell lines of different histology after exposure to taxanes is described below.
Materials and Methods Cell lines and clonogenic cell survival assays The growth characteristics clonogenic assay procedures of the 1 I human in vitro cell lines used in this analysis have already been reported e.g. in Britten R.A. and Warenius H., Eur. J. Canc. 29A, 1315-1320 (1993). The cell lines are listed, with their histological classiftcation in Table 2. All are well established; many having been growing in vitro for several years. Cell lines were either donations or purchased by our laboratories. On receipt all were grown for S passages to provide sufficient cells for batch storage in liquid nitrogen. During this period contamination was excluded by at least one passage in antibiotic free medium and mycoplasma testing was carried out on all lines.
For SUBSTITUTE SHEET (RULE 26) clonogenic assays, cells were taken from a designated primary liquid nitrogen batch and grown for 3-6 passages until there were sufficient well-growing cells. Further batches from these cells were frozen in liquid nitrogen. Cells were routinely maintained in DMEM medium. All lines were supplemented with 10% heat-inactivated foetal calf serum (HIFCS). Table 1 also shows relative values for cyclin D 1 levels in five human in vitro cell lines not expressing p21 and six human in vitro cell lines expressing p21. Also shown are the absolute and relative D0.1 values (i.e. the dose of the drug that reduces the clonogenic cell survival to 10% of the untreated control cells) for CDDP and taxoi. The D0.1 values were obtained by several independent clonogenic assays and the data fitted by linear regression analysis. The clonogenic assays were repeated until statistically satisfactory fits were achieved on linear regression. The D0.1 values were obtained by interpolation of the linear regression lines. The cytotoxic drug D0.1 values have been normalised and expressed as relative D0.1 values, to enable the relative sensitivity of each cell to each of the drugs to be compared. In order to normalise the values, the mean D0.1 was calculated independently for CDDP and taxol; each absolute D0.1 value was then adjusted by dividing by the mean value to give a relative DO.I value for each drug for each cell line.
The results set out in Table 1 are plotted in the graphs shown in Figures 1 and 2. Figure 1 shows relative D0.1 values for CDDP and taxol in five cell lines in which p21 protein was substantially undetectable. Three of the cell lines are relatively resistant to CDDP, but not to taxol. The remaining two cell lines which are less relatively resistant to CDDP are only slightly more sensitive to taxol than to CDDP. There would thus be an advantage in using taxol rather than cisplatin in the former three cell lines, but not in the latter two.
Figure 2 shows that there is no relationship between Cyclin D1 protein levels and relative sensitivity to CDDP in cells in which p21 protein is present in detectable quantities.
Moreover, some cell lines are relatively more resistant to taxol than CDDP.
Thus, in cell lines in which p21 protein is detectable, Cyclin DI is not a useful indicator either of resistance to CDDP or of whether the cell that would preferentially respond to taxol rather than CDDP.
SUBSTITUTE SHEET (RULE 26) Table 1 CDDP Taxol Undetectable p2I Relative CyclinAbsoluteRelativeAbsoluteRelative D 1 protein D0.1 D0.1 D0.1 D0.1 levels A431 3.21 (0.24)* 0.306 0.765 0.823 0.292 HT29 9.39 ( 1.47) 0.632 1.58 1.106 0.392 MOR 8.86 (0.87) 0.629 1.573 1.209 0.429 RT112 3.19 0.237 0.593 1.523 0.540 MEL2 7.32 0.457 1.143 0.57 0.202 Detectable p21 2780 4.42 (0.06) 0.255 0.637 2.113 0.749 I407 0.28 {0.01 0.06 0.15 1.504 0.537 ) HRT 18 4.44 (0.01 0.864 2.16 I 0.415 3.693 ) MGHU 1 6.23 (0.28) 0.4494 1.235 1.144 0.406 CORL23 2.11 (0.05) 0.338 0.845 0.497 0.176 OAW42 6.65 0.108 0.27 10.09? 3.581 *(tl S.E.M.) ' The Histology of the cell lines used in the above investigations is shown below in I
Table 2.
i SUBSTITUTE SHEET (RULE 26) Table 2 A431 Squamous carcinoma vulva HT29 Adenocarcinoma colon MOR Adenocarcinoma lung RT112 Transitional cell carcinoma bladder MEL2 Malignant melanoma 2780 Ovarian carcinoma I407 Embrionic intestinal epithelium HRT 18 Adenocarcinoma rectum MGHU 1 Transitional cell carcinoma bladder CORL23 Large cell lung carcinoma OAW42 Ovarian carcinoma In order to assay CDDP sensitivity 102-105 cells were plated in 3 ml of Ham's medium supplemented with 10% FCS in 6 well plates and incubated at 37°C
in an atmosphere of 5% C02 for 8 hours. Dilutions of 0.02-2.0 pg/ml from a 1 mg/ml stock solution of CDDP (light protected) were then made and 1 mi of the appropriate dilution were added to each plate to give a final volume of 4 ml. The plates were then incubated at 37°C in an atmosphere of 5% C02 in darkness for 14 days in the presence of the CDDP.
The medium was then removed, the cells were fixed in 70% ethanol and stained with 10% Giemsa and colonies of >100 cells counted. One 6 well plate was used for each drug dilution. A minimum of 3 separate clonogenic assays with 6 points/drug dose/assay were necessary for each cell line. CDDP cell survival was determined at the 10%
clonogenic cell survival level (D0.1 ) by interpolation of the fitted regression curve.
To measure taxol sensitivity, the same protocol as described above for CDDP
was employed, except an amphiphilic solubilising agent was added with the taxol.
Western Blotting for Cyclin Dl Two independent Western blottings with lysates for each cell line loaded in pairs on each gel were carried out. Standard conditions were used for the preparation of cells for SUBSTITUTE SHEET (RULE 26) lysates for Western blotting on each of the cell lines; 10' cells were grown in 162 cm2 tissue culture flasks (Costar Ltd., High Wycombe, Bucks) until they were pre-confluent but still growing exponentially as confirmed by flow cytometry. Cells were then removed by trypsinisation, re-suspended in complete medium +10% FCS and washed times by serial centrifugation and re-suspension in PBS without serum. 1-3 x I08 viable cells were then pelleted by centrifugation and re-suspended at 3x10' cells per ml of lysate buffer (Stock solution: 10% SDS lOml., O.SM Tris pH 6.8, glycerol 10 ml., Double distilled water 62 ml. . To 10 ml. of stock solution were added 100 ml of 10 mM
Leupeptin + 10 ml 100 mM PMSF). Protein estimations were performed and the final concentration of the lysates adjusted to 300 pg total cellular protein per 100 ~1. To measure cyclin D 1 protein, 1 SOpg of total cellular protein in 50.1 of lysate buffer were added per lane well to a 7.5% Laemmli separating gel and electrophoresis carried out at 16°C using 60V over 16 hours and a constant current of SOOmA. Blots were transferred to nitrocellulose at 22°C over 16 hours using to a semi-dry blotting apparatus (Biorad, Richmond, CA), incubated with the a mouse IgG, monoclonal antibody to mammalian cyclins (G124-259.5, Pharmingen) and then incubated with rabbit anti-mouse conjugated antibodies (Dako, UK) at 1/I000 and developed in alkaline phosphatase buffer containing Nitroblue Tetrazolium and 5-Bromo-4-Chloro-3-Indoyl Phosphate, (Sigma, Poole, Dorset, UK) (SOmg/ml in dimethylformamide) for 1 hr at room temperature in darkness.
Colour development was arrested with double distilled water, and the blots were dried flat. Cyclins were clearly resolved as distinct bands, cyclin D1 having the lowest mobility.
Quantitation of the protein product of the cyclin D 1 gene was carried out by measurement of optical density on a Schimadzu scanning densitometer with tungsten light and expressed as O.D. units per I SOpg of total cellular protein. Titration curves obtained by loading different amounts of total cellular protein have previously shown that linear relationships for optical density (O.D.) could be obtained over the range found for cyclin D1 protein across the cell lines (Warenius et al 1994, Browning 1997). In order to compare different cyclin D 1 protein levels between the cell lines, the mean O.D. value for all the lines was calculated and the relative O.D. for cyclin D 1 protein in each individual cell line was normalised to the mean O.D. and multiplied by an arbitrary value of 5Ø
SUBSTITUTE SHEET (RULE 26) In cell Iines in which p21 protein is undetectable, the more elevated the cyclin D 1 levels, the more resistant the cells are to the cytotoxic effects of chemotherapeutic agents other than taxanes (e.g. CDDP), but it is likely that these cells are instead sensitive to taxanes.
In other words, in cell lines in which p21 protein is undetectable, cyclin D1 over expression or elevated cyclin D 1 protein levels is an indicator that cells which are resistant to platinating agents will remain responsive to taxanes, whereas cell lines with low cyclin D 1 expression are likely to benefit from treatment with either taxanes or platinating agents (see Figure 1). However, the same correlation is not found in cells containing detectable quantities of p21 protein, in which some cell lines which are relatively resistant to CDDP are also resistant to taxanes, whilst others which are also relatively resistant to CDDP are sensitive to taxanes.
Accordingly, the present invention allows selection of an appropriate treatment for certain cancers by identifying the p21 level, and cyclin D1 expression or cyclin Dl protein level elevation in tumour cells; if platinating agents are ineffective for such cells, then a taxane is likely to be an effective agent for treatment of the cancer instead.
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SUBSTITUTE SHEET (RULE 26)

Claims

CLAIMS:

1. A method for selecting a chemotherapeutic agent for treating cancer, which method comprises:
(a) testing a sample comprising cells that substantially do not express p21 and/or in which p21 protein is substantially undetectable, or an extract therefrom for the level of expression of Cyclin D1 or for the abundance of cyclin D1 protein; and (b) if cyclin D1 is overexpressed, and/or cyclin D1 protein is present at elevated levels, selecting for treatment a chemotherapeutic agent comprising a taxane;
(c) if cyclin D1 is not overexpressed and/or cyclin D1 protein is substantially not present at elevated levels, selecting for treatment a chemotherapeutic agent comprising an agent other than a taxane.

2. A method according to claim 1, wherein the chemotherapeutic agent is selected according to step (b), and the taxane comprises taxol.

3. A method according to claim 1, wherein the chemotherapeutic agent is selected according to step (c), and the agent other than a taxane comprises a platinating agent.

4. A method according to claim 2, wherein the chemotherapeutic agent selected for treatment further comprises a platinating agent.

5. A method according to claim 3, wherein the chemotherapeutic agent selected for treatment further comprises a taxane.

6. A method according to any preceding claim, wherein the sample is extracted from a subject.

7. A method according to any preceding claim, wherein the testing for the abundance of cyclin D1 protein comprises measuring the abundance of cyclin D1 mRNA.

8. A method according to claim 7, wherein the measurement of the abundance of cyclin D1 mRNA comprises contacting the sample with a probe for cyclin D 1 mRNA.

9. A method according to any of claims 1-6, wherein the testing for the abundance of cyclin D 1 protein is carried out using Western blotting.

10. A method according to any of claims 1-6, wherein the testing for the abundance of cyclin D1 protein comprises contacting the sample with a labelled antibody against cyclin D1 protein.

11. A method according to claim 10, wherein the antibody against cyclin D1 protein is 14841 C (from clone number G-124-259.5, Pharmingen USA).

12. A method according to claim 10 or claim 11, wherein at least one antibody is labelled with a fluorescent label.

13. A method according to any preceding claim, further comprising contacting the sample with a DNA binding dye for labelling aneuploid cells.

14. A method according to claim 13, wherein the DNA binding dye is Hoechst 33258, or Chromomycin A3 dye.

15. A method according to any preceding claim, wherein the sample is a sample of cells.

16. A method according to claim 15, wherein the testing is carried out by performing a cell count.

17. A method according to claim 16, wherein the cell count is performed using multi-parameter flow cytometry.

18. A method according to claim 16, wherein the cell count is performed using scanning confocal microscopy.

19. A method according to claim 16, wherein the cell count is performed using fluorescence activated cell sorting.

20. A method according to any of claims 16-19, wherein the sample of cells is micra-dissected prior to performing the cell count, to separate normal tissue from tumour tissue.

21. A method according to any of claims 16-20, wherein prior to performing the cell count, intracellular adhesion in the sample of cells is disrupted, to form a single cell suspension.

22. A method according to any preceding claim, for selecting either an agent comprising a taxane, or an agent comprising a platinating agent, for treating cancer.

23. A kit for selecting a chemotherapeutic agent for treatment, which kit comprises:
(a) a means for identifying cells in which p21 is substantially not expressed and/or p21 protein is substantially undetectable; and (b) a means for testing for the level of expression of Cyclin D1 or for the abundance of cyclin D1 protein in cells or in a sample therefrom.

24. A kit according to claim 23, for selecting either an agent comprising a taxane, or an agent comprising a compound other than a taxane such as a platinating agent, for treating cancer.

25. A kit according to claim 23 or claim 24, wherein the means for testing for the abundance of cyclin D 1 protein comprises a probe for cyclin D1 mRNA.

26. A kit according to claim 23 or claim 24, wherein the means for testing for the abundance of cyclin D1 protein comprises a labelled antibody against cyclin D1 protein.

27. A kit according to claim 26, wherein the antibody against cyclin D1 protein is 14841 C (from clone number G-124-259.5, Pharmingen USA).

28. A kit according to claim 26 or 27, wherein at least one antibody is labelled with a fluorescent label.

29. A kit according to any of claims 23-28, further comprising a DNA binding dye, for labelling aneuploid cells.

30. A kit according to claim 29, wherein the DNA binding dye is Hoechst 33258, or Chromomycin A3 dye.

31. Use of a means for identifying cells in which p21 is substantially not expressed and/or p21 protein is substantially undetectable, for selecting either an agent comprising a taxane, or an agent comprising a platinating agent, for treating cancer.

32. Use of a means for testing for the level of expression of Cyclin D1 or for the abundance of cyclin D1 protein in cells or in a sample therefrom, for selecting either an agent comprising a taxane, or an agent comprising a platinating agent, for treating cancer.